- Northern Blot
- Agarose gel electrophoresis 

Methods of Visualizing RNA

Like DNA, RNA can be visualized using various methods in the lab. From this, we can observe the different sizes of RNA and observe the different sizes and amounts of mRNA produced in different cellular tissues.

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RNA is involved in protein synthesis and regulation. It also has catalytic properties.
RNA is typically found in the single stranded form.
RNA is formed from hydrogen bonds between the base pairs adenine and uracil and cytosine and guanine bases, respectively.

Ribonucleic Acid (RNA)

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- Most commonly single stranded but can be double stranded as well 
- RNA contains ribose sugar which contains an extra OH group compared to DNA (deoxyribose) 
- RNA can form more shapes and conformations than DNA and it can be catalytic
- All RNA come from DNA template however, because it can bind to the DNA template. 


RNA structure

- Transcription is initiated by a promoter – about 40 base pair sized sequences starting on the 5’ end of the start site. 
- -10 and -35 sequence is  the promoter sequence, while initiation occurs downstream  (add image)
- Initiation requires formation of transcription bubble 
- Sigma factors – determine which genes are transcribed. 
– In some bacteria, sigma factors can differentiate when genes are expressed as early, middle, and late genes. 


Prokaryotic RNA transcription (Initiation)

- RNA transcription in eukaryotes differs from prokaryotes in that it has many RNA polymerases and it has a more complex control sequence.  
- Numbers of RNA Polymerases:
   - RNA polymerase 1 – synthesizes the precursor to mRNA 
   - RNAP II – synthesizes mRNA precursors 
   - RNAP III- synthesizes precursors to 5S rRNA (subunit of ribosome), tRNA, and smaller RNAs. 
   - Mitochondrial and chloroplasts RNA polymerases are also present . 
- These all recognize different promoters as well. However core promoters are the TATA box that is present 25-31 base pairs upstream of the transcription start site. 
- Enhancers – are recognized by transcription factors that attract RNA polymerase II to bind to a nearby promoter. These are important in selective gene expression. 
- Transcription factors initiation transcription by binding specifically to the promoters of DNA. This is a same process in eukaryotes and prokaryotes. 
- At the TATA box a preinitaiton complex forms with the RNA polymerase transcription factors and the DNA promoter region. 
- The TATA binding protein binds to the TATA box. It forms a TFIID complex with 17 other proteins. 

Eukaryotic RNA Transcription (Initiation)

Ribosomal RNAs or rRNAs make up about 50% of the ribosome. They are structural or enzymatic and are important in forming the ribosome to be used for translation. They are also a product of transcription.

rRNA

Transfer RNAs or tRNAs translate the mRNA code to the corresponding amino acids by binding to the specific codons. There are many types depending on the species. They are also a product of RNA transcription.

tRNA

Antisense RNA are complementary regions of mRNA molecules. It is a type of non-coding RNA.

Antisense RNA

Messenger RNA (mRNA) is one product of transcription. It has the genetic information needed to synthesize proteins during translation.

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